Precisely Controlled Smart Polymer Scaffold for Nanoscale Manipulation of Biomolecules

Abstract

ABSTRACT:We demonstrate the application of a novel smart surface to modulate the orientation of immobilized double stranded DNA (dsDNA) and the conformation of a polymer scaffold through variation in buffer pH and ionic strength. An amphoteric poly(dimethylacrylamide) based coating containing weak acrylamido acids and bases, which are copolymerized together with the neutral monomer, is covalently bound to the surface. The coating can be made to contain any desired amount of buffering and titrant ionogenic monomers, allowing control of the surface charge when the surface is bathed in a given buffer pH. Spectral self-interference fluorescence microscopy (SSFM) is utilized to precisely quantify both the DNA orientation and the polymer conformation with subnanometer resolution. It is possible to utilize the polymer scaffold to functionalize a variety of common materials used in microfabrication, making it a general purpose building block for the next generation of nanomachines and biosensors.

Activated Ester Containing Polymers: Opportunities and Challenges for the Design of Functional Macromolecules

“…Similarly, PNPA has been utilized for the formation of functional hydrogel layers . Rather than pretreating the glass surface with 3-(trimethoxysilyl)­propyl methacrylate, direct copolymerization of dimethylacrylamide, 3-(trimethoxysilyl)­propyl methacrylate, and NHSA (Scheme ) led to polymers that allow direct deposition of activated ester-containing polymers onto substrates. ,, Similar surface functionalizations have been achieved with the tercopolymer prepared from NHSA, 3-(trimethoxysilyl)­propyl methacrylate, and PEGMA or other variations to alter surface wetting properties − or enable biomolecule conjugation. , In particular, this approach has been used for the preparation of DNA microarray sensors. ,− The biocompatibility of these approaches has also led to the exploration of NHSA in dental adhesives …”

A Reliable, Label Free Quality Control Method for the Production of DNA Microarrays with Clinical Applications

“…Furthermore, DNA is well-known to have a net negative charge. In Spuhler P. et al [28] we have demonstrated that the combination of DNA negative charges, together with the remaining charges on the coated surface (with this particular ionic strength environment) are enough to generate significant elevation of the probe. However, probes different from DNA (such as protein or peptide) have more functionalities in their structure which may interact with the surface, leading to non-specific binding, thus causing loss of activity and reduced probe conformational flexibility.…”

Spectral Self-Interference Fluorescence Microscopy to Study Conformation of Biomolecules with Nanometer Accuracy

“…The isoelectric point of the polymer was tested to be around pH 6 by electroosmotic flow in a capillary coated by a polymer with identical composition. Lower buffer pH results in a net positively charged surface, attracting dsDNA to the surface, whereas higher buffer pH results in a net negatively charged surface, repelling dsDNA to a higher orientation to the surface [111]. An overview of the manipulation of dsDNA orientation on a charged polymer surface through adjustment of buffer pH and ionic strength is shown in Figure 9.10a.…”